The Molecular Inversion Probe technology has been developed to allow 1000 SNPs to be called in a single tube. This technology holds the promise of enabling large scale inexpensive genetic analysis including the analysis of whole genomes. Before such studies can be contemplated, further platform development is required. Software tools must be developed to process MIP technology data and interface with a LIMS database to ensure data and process integrity. With this in place, a pilot scale study will be conducted. The applicants have formed a collaboration with a group at Yale University who have samples from a population that is afflicted with IgA nephropathy, a debilitating kidney disorder which has been linked to genetic factors on Chromosome 6. A pilot scale study is described that would allow the MIP technology to be applied to a real world association study. Concurrently, automation will be developed that will allow high throughput operations of both the chip processing and assay fluid handling. Researchers at the SGTC will play a central role in developing the hardware necessary for this task. Finally, additional functionality will be added by increasing the level of spectral multiplexing for the chip detection (which will decrease the cost and increase the data quality) and increasing the level of SNP multiplexing (which will decrease the usage of DNA and increase the compactness of the operation). These developments will increase the SNP throughput at ParAllele to >500,000 SNPs/day and provide the basis for a new enabling technology. This application represents a Phase II proposal that follows on from a funded STTR grant. During Phase I, the applicants successfully exceeded the development milestones that were set. The targets of developing a 100plex assay with >98% accuracy and 95% call rate were met with a 1000plex assay with 97% call rate and >99% accuracy. We hope that the demonstrated success of this academic/industrial partnership will enable further development to be funded at the level requested.